Align methylmalonyl-CoA mutase (subunit 2/2) (EC 5.4.99.2) (characterized)
to candidate CA265_RS14780 CA265_RS14780 methylmalonyl-CoA mutase
Query= BRENDA::O74009 (563 letters) >FitnessBrowser__Pedo557:CA265_RS14780 Length = 1129 Score = 228 bits (580), Expect = 1e-63 Identities = 142/370 (38%), Positives = 219/370 (59%), Gaps = 12/370 (3%) Query: 195 LRGTVQNDILKEYIARGTYIFPPQPSMRLTTDIIMYCA-ENVPKWNPISISGYHIREAGA 253 +RGTVQ DILKE A+ T IF + ++R+ DI Y E V + +SISGYHI EAGA Sbjct: 763 VRGTVQADILKEDQAQNTCIFSTEFALRMMGDIQKYFIDEKVRNFYSVSISGYHIAEAGA 822 Query: 254 NAVQEVAFTLADGIEYVKAVIERGMDVDKFAPRLSFFFAAHNNFLEEIAKF-RAARRLWA 312 N + ++AFTL++G +V+ + RGM +D FAP LSFFF+ N E A R ARR+WA Sbjct: 823 NPISQLAFTLSNGFTFVEYYLSRGMHIDDFAPNLSFFFS--NGIDPEYAVIGRVARRIWA 880 Query: 313 YIMKEWFNAKNPRSMMLRFHTQTAGSTLTAQQPENNIVRVAIQALAAVLGGTQSLHTNSY 372 +K + N RS L++H QT+G +L AQ+ + N +R +QAL A+ SLHTN+Y Sbjct: 881 KAIKNKYKG-NDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAY 939 Query: 373 DEALSLPTEKSVRIALRTQQIIAYESGVVDTVDPLGGAYYIEWLTDHIYEEALKYIEKIQ 432 DEA++ PTE+SVR A+ Q II E G+ +PL GA+ IE LTD + + L ++I Sbjct: 940 DEAITTPTEESVRRAMAIQLIINRELGLAKNENPLQGAFIIEELTDLVEDAVLAEFKRIN 999 Query: 433 KMGGMMRAIERGYVQKEIAEAAYKYQKEIEEGKRIIVGVNAFVTDEP----IEVEILKVD 488 GG++ A+E Y + +I E + Y+ G+ IVGVN F+ + E+++ Sbjct: 1000 DRGGVLGAMETMYQRGKIQEESLYYETLKHTGEYPIVGVNTFLNKNGSPTIVPGEVIRAT 1059 Query: 489 PSIREKQIERLKKLRSERDNKKVQEALDKLRNAAEKEDENLMPYIIEAHRHLATLQEVTD 548 ++ QI L+K + +R+ + + L +L+ +A D N+ ++E + + +L +++ Sbjct: 1060 EDEKQYQISALQKFQ-DRNADRAVDLLKQLQKSAIAGD-NIFEQLMEVCK-ICSLGQISK 1116 Query: 549 VLREIWGEYR 558 L E+ G+YR Sbjct: 1117 ALYEVGGQYR 1126 Score = 75.5 bits (184), Expect = 1e-17 Identities = 67/226 (29%), Positives = 108/226 (47%), Gaps = 16/226 (7%) Query: 6 KEVLKKIKEEEKRW-EETTVKKFLEKAPERKEKFMTDDGFEIKRIYTPA--DLGEDWNYM 62 K +L++ + ++ + EE + K +K ++ + + I ++ P D G+ ++ Sbjct: 502 KRLLRQWPDTKRAYKEEFFIYKVRDKEIKQPLFYESLSKLNIPKVSLPRYEDWGDILRWL 561 Query: 63 EKLGFPGEYPFTRGVYATMYRGRIWTMRQYAGYATAEESNKRYKYL-LSQGQTGLSVAFD 121 PGE+P+ GV+ G T R +AG E +NKR+ Y+ L Q LS AFD Sbjct: 562 LTENLPGEFPYAAGVFPLKREGEDPT-RMFAGEGGPERTNKRFHYVSLGQPAHRLSTAFD 620 Query: 122 LPTQLGYDSD-HPLAEGEVGKVGVAIDSLWDMRILFDGIPL--DKVSTSMTINSTAANLL 178 T G D P G++G GV I +L D + L+ G L S SMTIN A LL Sbjct: 621 SVTLYGEDPHIRPDIYGKIGNSGVCIATLDDAKKLYSGFDLCAPSTSVSMTINGPAPMLL 680 Query: 179 AMYILVAEEQGVSQEKLRGTVQNDILKEYIARGTYIFP----PQPS 220 ++ A + Q+ + ++ND+ KE A+ I+ P+PS Sbjct: 681 GFFMNAA----IDQQCEKYIIENDLTKEVEAKIDAIYQAKNIPRPS 722 Lambda K H 0.318 0.134 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1304 Number of extensions: 67 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 563 Length of database: 1129 Length adjustment: 41 Effective length of query: 522 Effective length of database: 1088 Effective search space: 567936 Effective search space used: 567936 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory